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Table 2 Identified genes with known GO terms with a P ≤ 0.05 and ≥ 2-fold changes

From: Medulla oblongata transcriptome changes during presymptomatic natural scrapie and their association with prion-related lesions

 

Preclinical stage

Clinical stage**

Term

P-Value

Probe Name

Gene symbol

Gene name

FC

Compositionally biased region

4.90E-02

A_70_P049406

EIF5

Eukaryotic translation initiation factor 5, transcript variant 7

−2.65

−1.94

External side of plasma membrane

4.60E-02

A_70_P048131

GPC3

Glypican 3

−2.95

−2.56

Extracellular matrix binding

5.30E-02

A_70_P050511

NID1

Nidogen 1

−2.78

−4.15

Extracellular matrix organization

1.90E-02

A_70_P059746

CYR61

Cysteine-rich, angiogenic inducer, 61

−2.97

−3.42

A_70_P061221

P4HA1

Prolyl 4-hydroxylase, alpha polypeptide I

−3.00

−2.81

Granzyme A mediated Apoptosis Pathway

6.20E-02

A_70_P054526

ANP32A

Acidic (leucine-rich) nuclear phosphoprotein 32 family, member A

−2.86

−2.47

A_70_P040956

GZMB

Granzyme B

−3.10

NSR

MHC protein binding

4.90E-02

A_70_P016891

CD3G*

CD3 Gamma chain

−3.20

NSR

A_70_P008201

CLEC7A

C-type lectin domain family 7, member A

−2.20

NSR

CUST_12481_PI375351158

TRD@

T-cell receptor delta chain

−3.30

NSR

Organelle lumen

6.80E-02

A_70_P037521

FGB

Fibrinogen beta chain

−2.44

NSR

A_70_P020146

MRPL39

Mitochondrial ribosomal protein L39

−2.37

NSR

A_70_P036101

NOP10

NOP10 ribonucleoprotein homolog (yeast) (NOP10), mRNA

−3.34

NSR

A_70_P007556

SUMF1

Sulfatase modifying factor 1

−2.11

NSR

Phosphoprotein

1.30E-03

A_70_P037146

ACOX3

Acyl-Coenzyme A oxidase 3, pristanoyl

−2.23

−1.73

A_70_P021671

ARPC3

Actin related protein 2/3 complex, subunit 3, 21 kDa

−2.46

NSR

A_70_P019041

ATP8B2

Similar to ATPase, class I, type 8B, member 2

−2.19

−1.78

A_70_P024516

CDKN1B

Cyclin-dependent kinase inhibitor 1B (p27, Kip1)

−2.03

−1.71

A_70_P001561

FOS

FBJ murine osteosarcoma viral oncogene homolog

−2.86

−2.66

A_70_P008036

LAPTM4A

Lysosomal protein transmembrane 4 alpha

−2.58

−2.10

A_70_P018586

LAPTM4B*

Lysosomal protein transmembrane 4 beta

−3.65

−2.80

A_70_P049041

MAT2A

Methionine adenosyl transferase II, alpha

−2.24

−1.63

A_70_P006536

MGMT

PREDICTED: O-6-methylguanine-DNA methyltransferase

−2.89

−2.22

A_70_P030701

NES

Nestin

2.02

2.55

A_70_P026261

SLC16A1

Solute carrier family 16, member 1 (monocarboxylic acid transporter 1)

−2.65

−2.34

A_70_P027206

SLC30A1

Solute carrier family 30 (zinc transporter), member 1

2.45

2.27

A_70_P018386

SLC44A1

CDW92 antigen, transcript variant 2

−2.27

NSR

A_70_P059781

UBE2E1

Ubiquitin-conjugating enzyme E2E 1, transcript variant 2

−2.31

NSR

A_70_P031441

VCL

Vinculin, transcript variant 2

−2.01

NSR

A_70_P022731

WDR33

WD repeat domain 33

−2.54

NSR

A_70_P033291

LOC618584

Zinc finger, CCHC domain containing 2

−2.08

−1.87

A_70_P043106

ZNF428

Zinc finger protein 428, transcript variant 2

−2.28

−2.27

Response to a biotic stimulus

4.00E-02

CUST_10550_PI375351158

BTG2

B cell translocation protein 2

−2.41

NSR

Response to fungus

4.90E-02

A_70_P050991

GNLY*

Granulysin

−3.97

NSR

Tight junction assembly

5.60E-02

A_70_P003466

MPP7

membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7) (MPP7), mRNA

2.93

NSR

  1. Shown are the Blast results of the clones with significant alterations in gene expression (P ≤ 0.05 and ≥ 2-fold change). FC of significant alteration during clinical stage is given in the last column (NSR: no significant regulation). The GO was determined using on-line functional annotation of DAVID Bioinformatics Resources 2008 (NIAID/NIH, USA). Only the genes with a known GO are shown.
  2. *Genes chosen for validation by quantitative RT-PCR.
  3. **FC values obtained in a previous study developed by our group comparing scrapie-infected animals in a clinical stage and controls[25].
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BMC Genomics

ISSN: 1471-2164

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